I've discussed at length my problems with keeping OneNote in sync across machines. I've finally settled on FolderShare which has worked almost flawlessly for my personal machines but unfortunately is blocked at work.
Chris Pratley discusses a few of the options for keeping your OneNote 2007 data synchronized across machines. OneNote 2007 allows you to have shared notebooks - for one project, I'm sharing a notebook with four others hosted on a Sharepoint site. Unlike OneNote 2003, it's actually pretty efficient and (generally) works when you're disconnected as well. (I've had a few hiccups, but this was with early Beta software, so hopefully it is ironed out by release).
I actually just finished setting up a test server with, among other things, Groove Server and Sharepoint 2007 Beta2. I'm hoping to spend some time with it this weekend and see if it brings anything additional to the table.
The good news is that the OneNote team seems well aware of these problems and has done some good things to help fix it.